Africa's first and only female president Liberia's Ellen Johnson Sirleaf was re-elected on Thursday with 90.2% of the vote, but her government may struggle to prove its legitimacy because the opposition boycotted the poll.

Hours before the results were announced in an election that was supposed to solidify Liberia's shaky peace, opposition leader Winston Tubman said he would not accept the outcome of this week's presidential runoff.

With nearly nine-tenths of precincts reporting, National Election Commission chair Elizabeth Nelson said that Sirleaf had received 513,320 votes out of 565,391 tallied. Only 52,071 ballots, or 9.2%, had been cast for Tubman, a former United Nations diplomat who, like Sirleaf, was educated at Harvard University.

Last week, Tubman, who is the nephew of Liberia's longest-serving president, William Tubman, called on his supporters to boycott Tuesday's presidential runoff. By early morning, many polling stations had no queues outside. By afternoon, poll workers were seen dozing, some laying their heads on tables next to near-empty ballot boxes.

Turnout hovered around 37% of registered voters, just over half of the 71% who turned out for the election's first round.

However Sirleaf, who was jointly awarded the Nobel peace prize this year, said Liberia's elections "were legitimate". Tubman's allegations of fraud were largely unsubstantiated by the almost 5,000 national and international election observers in the country. The Carter Centre's election observer mission said there was "no evidence of significant irregularities or systematic fraud". However, thousands of CDC supporters did as their leader commanded and stayed at home.

Most analysts believe that Tubman would have lost Tuesday's election if he had participated. "If you look at the figures, you can see that Tubman [was] almost certainly going to lose. He is 12, 13 points down in the polls," said Stephen Ellis, a researcher at the African Studies Centre, Leiden in the Netherlands.

"It's an obvious calculation. He withholds legitimacy from the government," Ellis said. "If it was felt by a large part of population to not be legitimate, in a place like Liberia, with its history, it becomes quite worrying."

Other analysts expressed fears the result would dent the credibility of Sirleaf's government. "The government will need to strengthen the belief and participation in democracy to win back the people," said Abdullai Kamara, a media and democracy analyst based in Monrovia. "There was no competitor so it didn't give people any impetus to go out and vote."

It was not only the "one party" race that failed to entice people to the polls, it was also fear. The day before the vote, the CDC organised a protest march intended to be peaceful at its headquarters, but it ended in bloodshed. CDC supporters began throwing stones and bottles at the police, who then responded with teargas and live ammunition on the crowd.

While Tubman and his running mate, the former Milan and Chelsea footballer George Weah, were trapped inside the compound, at least two people were shot dead and more than five were wounded.

"People were afraid to come out and vote," said Alsena Jones, 31. The mother- of-two, a Sirleaf supporter, said she was delighted that her candidate would stay in power but she couldn't stop thinking about the violence. "I feel very happy but sad after what went on on Monday when Liberians lost their lives."

However her neighbour Nelson Winston, 20, a CDC supporter, said once Sirleaf was officially announced the winner he would be happy to accept her as his president. "I'm a peaceful Liberian and I know what the war did to us," he said. "For me, once Sirleaf is announced as the winner, I have no problem with it,' he said. "I'm CDC but it doesn't mean I'll go on the street. I would never do that."

Liberia has been praised for its fledgling democracy after 14 years of brutal civil war that claimed more than 250,000 lives.

In the last two weeks, the CDC has repeatedly said it would not recognise the results of the election, but speaking to the Guardian its national director for policy and communications, Rich Urey, said the party would sit "at the table [with Sirleaf] to decide the future of Liberia".

He ruled out the possibility of power sharing but said they think "there should be equity in the decision making process of the country".

Just before the results were announced, Sirleaf said "We intend to reach out to all the CDC leaders,' she said. "We have to make sure there is reconciliation."